Description

Constructs a graph from a reference and variant calls or a multiple sequence alignment file

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

input (file(s))

Either one or more VCF files containing different contigs or a multiple sequence alignment file

*.{vcf.gz,fa,fasta,fna,clustal}

tbis (file(s))

The index files for the VCF files

*.tbi

insertions_fasta (file)

A FASTA file containing insertion sequences (referred to in the VCF file(s))

*.{fa,fasta,fna}

fasta (file)

The reference FASTA file (cannot be used in combination with msa, but is required when using vcfs)

*.{fa,fasta,fna}

fasta_fai (file)

The index of the reference FASTA file

*.fai

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

graph (file)

The constructed graph

*.vg
maintainer
Github user nvnieuwk
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Tools

vg
MIT

Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods.

github.com/vgteam/vg github.com/vgteam/vg/wiki